A program that I have had good success with is Dr Web. I usually only use the Live CD boot disk, but it has found viruses and rootkits when NOTHING else has worked and found viruses and malware when nothing else did on more than one system I have had to triage.

I like it a little better because you get a fully functional Linux Boot disc that is self-updating so you will always use the most current DB when you have to scan. There is a standard Windows based scanner program that works very well also, but I have found that I like their Boot Disc / Rescue CD better than any other I have tested. Since Bart PE does not have something that I consider really good, I use this instead of booting into Bart PE. Booting into Linux also gives you a little more functionality than Bart PE, for the most part.

And, like everything else I like, it's FREE.

http://www.freedrweb.com/livecd/